Object properties for just a specific object with python?
Your property is being created for the scenes, when you want to create it for the objects. So this:

bpy.types.Scene.IntCheckpoint


needs to be changed to this:

bpy.types.Object.IntCheckpoint


And then in your panel you'll change this:

col.prop(scene, "IntCheckpoint")


to this:

col.prop(obj, "IntCheckpoint")


So to create a property specific to a type, you have to use that type in your property declaration.